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Summary Geometry Related PDB entries

K6U

Bonds

First atom	Second atom	Bond order type	Distance (experimental model)	Distance (ideal model)	Properties
C1	O1	sing	1.43Å	1.42Å
O1	C2	sing	1.36Å	1.37Å
C2	C3	doub	1.38Å	1.39Å	Aromatic
C3	C4	sing	1.38Å	1.38Å	Aromatic
C4	C5	doub	1.38Å	1.38Å	Aromatic
C5	C6	sing	1.38Å	1.38Å	Aromatic
C6	C7	doub	1.39Å	1.39Å	Aromatic
C7	C8	sing	1.48Å	1.46Å
C8	N1	doub	1.31Å	1.29Å	Aromatic
N1	N2	sing	1.29Å	1.42Å	Aromatic
N2	C9	doub	1.30Å	1.27Å	Aromatic
C9	O2	sing	1.34Å	1.35Å	Aromatic
C2	C7	sing	1.40Å	1.40Å	Aromatic
C8	O2	sing	1.35Å	1.37Å	Aromatic
C4	H5	sing	1.08Å	1.08Å
C5	H6	sing	1.08Å	1.08Å
C6	H7	sing	1.08Å	1.08Å
C1	H3	sing	1.09Å	1.10Å
C1	H2	sing	1.09Å	1.10Å
C1	H1	sing	1.09Å	1.10Å
C3	H4	sing	1.08Å	1.08Å
C9	H8	sing	1.08Å	1.08Å

Angles

First atom	Second atom	Third atom	Angle (experimental model)	Angle (ideal model)
C1	O1	C2	119.5°	116.9°
O1	C1	H3	109.5°	109.5°
O1	C1	H2	109.5°	109.5°
O1	C1	H1	109.5°	109.4°
O1	C2	C3	123.7°	120.2°
O1	C2	C7	116.4°	120.1°
C2	C3	C4	120.1°	120.1°
C3	C2	C7	119.8°	119.7°
C2	C3	H4	120.0°	120.0°
C3	C4	C5	120.6°	120.4°
C3	C4	H5	119.7°	119.9°
C4	C3	H4	119.9°	120.0°
C4	C5	C6	119.9°	120.3°
C5	C4	H5	119.7°	119.8°
C4	C5	H6	120.1°	119.9°
C5	C6	C7	121.1°	119.9°
C6	C5	H6	120.0°	119.8°
C5	C6	H7	119.5°	120.0°
C6	C7	C8	119.0°	120.2°
C6	C7	C2	118.5°	119.7°
C7	C6	H7	119.4°	120.1°
C7	C8	N1	131.1°	126.4°
C8	C7	C2	122.5°	120.1°
C7	C8	O2	119.1°	126.4°
C8	N1	N2	106.3°	109.3°
N1	C8	O2	109.8°	107.2°
N1	N2	C9	107.9°	109.5°
N2	C9	O2	110.3°	107.7°
N2	C9	H8	124.9°	126.2°
C9	O2	C8	105.7°	106.3°
O2	C9	H8	124.8°	126.1°
H3	C1	H2	109.5°	109.5°
H3	C1	H1	109.5°	109.5°
H2	C1	H1	109.5°	109.5°

Dihedrals

First atom	Second atom	Third atom	Fourth atom	Torsion (experimental model)	Torsion (ideal model)
C1	O1	C2	C3	66.1°	0.0°
C1	O1	C2	C7	117.1°	179.6°
O1	C1	H3	H2	120.0°	120.1°
O1	C1	H3	H1	120.0°	119.9°
O1	C1	H2	H1	120.0°	120.0°
O1	C2	C3	C7	176.7°	179.6°
O1	C2	C3	C4	178.6°	180.0°
O1	C2	C7	C6	179.3°	179.8°
O1	C2	C7	C8	3.5°	0.1°
C2	O1	C1	H3	180.0°	60.0°
C2	O1	C1	H2	60.0°	60.0°
C2	O1	C1	H1	60.0°	180.0°
O1	C2	C3	H4	1.4°	0.5°
C2	C3	C4	H4	180.0°	179.5°
C2	C3	C4	C5	0.7°	0.5°
C3	C2	C7	C6	2.3°	0.2°
C3	C2	C7	C8	179.5°	179.7°
C2	C3	C4	H5	179.3°	179.8°
C3	C4	C5	H5	180.0°	179.7°
C3	C4	C5	C6	0.1°	0.3°
C4	C3	C2	C7	1.9°	0.5°
C3	C4	C5	H6	179.9°	179.7°
C4	C5	C6	H6	180.0°	180.0°
C4	C5	C6	C7	0.3°	0.0°
C4	C5	C6	H7	179.7°	180.0°
C5	C4	C3	H4	179.3°	180.0°
C5	C6	C7	H7	180.0°	180.0°
C5	C6	C7	C8	178.8°	180.0°
C5	C6	C7	C2	1.5°	0.0°
C6	C5	C4	H5	179.9°	179.9°
C6	C7	C8	C2	177.2°	179.9°
C6	C7	C8	N1	24.0°	180.0°
C6	C7	C8	O2	153.8°	0.0°
C7	C6	C5	H6	179.7°	180.0°
C7	C8	N1	O2	178.0°	180.0°
C7	C8	N1	N2	178.8°	180.0°
C7	C8	O2	C9	179.1°	180.0°
C8	C7	C6	H7	1.2°	0.1°
C8	N1	N2	C9	0.5°	0.0°
N1	C8	O2	C9	0.8°	0.0°
N1	C8	C7	C2	158.8°	0.1°
N1	N2	C9	O2	0.0°	0.0°
N2	N1	C8	O2	0.8°	0.0°
N1	N2	C9	H8	179.9°	180.0°
N2	C9	O2	H8	180.0°	180.0°
N2	C9	O2	C8	0.5°	0.0°
C2	C7	C8	O2	23.4°	179.9°
C2	C7	C6	H7	178.5°	180.0°
C7	C2	C3	H4	178.1°	180.0°
C8	O2	C9	H8	179.5°	180.0°
H5	C4	C5	H6	0.2°	0.1°
H5	C4	C3	H4	0.6°	0.3°
H6	C5	C6	H7	0.3°	0.0°
H3	C1	H2	H1	120.0°	120.0°

249697

PDB entries from 2026-02-25

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